Point and interval estimates of abundance using multiple covariate distance sampling: an example using great bustards.

Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000447/The pdf file contains the tech report, the ASCII (.R) file contains the accompanying R code.Description of computations to produce sex-specific estimates of density from a multiple-covariate distance sampling analysis. Program Distance 5.0 has limited capacity to bootstrap certain types of analytical situations (e.g., cluster size as a covariate). Herein I describe steps and code to perform an analysis of this sort. Possible ways to adapt this code for similar analyses are described.Postprin

Animal Counting Toolkit : a practical guide to small-boat surveys for estimating abundance of coastal marine mammals

The authors thank Synchronicity Earth, Marisla Foundation, and the US Marine Mammal Commission for seed funding for this program.Small cetaceans (dolphins and porpoises) face serious anthropogenic threats in coastal habitats. These include bycatch in fisheries; exposure to noise, plastic and chemical pollution; disturbance from boaters; and climate change. Generating reliable abundance estimates is essential to assess sustainability of bycatch in fishing gear or any other form of anthropogenic removals and to design conservation and recovery plans for endangered species. Cetacean abundance estimates are lacking from many coastal waters of many developing countries. Lack of funding and training opportunities makes it difficult to fill in data gaps. Even if international funding were found for surveys in developing countries, building local capacity would be necessary to sustain efforts over time to detect trends and monitor biodiversity loss. Large-scale, shipboard surveys can cost tens of thousands of US dollars each day. We focus on methods to generate preliminary abundance estimates from low-cost, small-boat surveys that embrace a ‘training-while-doing’ approach to fill in data gaps while simultaneously building regional capacity for data collection. Our toolkit offers practical guidance on simple design and field data collection protocols that work with small boats and small budgets, but expect analysis to involve collaboration with a quantitative ecologist or statistician. Our audience includes independent scientists, government conservation agencies, NGOs and indigenous coastal communities, with a primary focus on fisheries bycatch. We apply our Animal Counting Toolkit to a small-boat survey in Canada’s Pacific coastal waters to illustrate the key steps in collecting line transect survey data used to estimate and monitor marine mammal abundance.Publisher PDFPeer reviewe

Occurrence of flat bugs (Heteroptera: Aradidae) in burned and unburned forests

The goal of this study was to determine the effect of fire on flat bug diversity and abundance in coniferous and mixed forests in interior Alaska. Eighty individuals, of which 78 in the burned areas and two in the control areas, of six aradid species were collected: Aradus abbas (Bergroth), A. funestus (Bergroth), A. lugubris (Fallén), A. signaticornis (Sahlberg), A. tuberculifer (Kirby) and Aneurus simplex (Uhler). Generally, all flat bug species were more abundant in the burned areas than in control areas with statistically significant differences for four of the six species and for pooled nymphs. Habitat preferences and potential mechanisms connecting mycophagy and pyrophagy are discussed

Distance sampling in R

Estimating the abundance and spatial distribution of animal and plant populations is essential for conservation and management. We introduce the R package Distance that implements distance sampling methods to estimate abundance. We describe how users can obtain estimates of abundance (and density) using the package as well as documenting the links it provides with other more specialized R packages. We also demonstrate how Distance provides a migration pathway from previous software, thereby allowing us to deliver cutting-edge methods to the users more quickly.Publisher PDFPeer reviewe

Distance software: design and analysis of distance sampling surveys for estimating population size

1.Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance

Weather-driven change in primary productivity explains variation in the amplitude of two herbivore population cycles in a boreal system

Vertebrate populations throughout the circumpolar north often exhibit cyclic dynamics, and predation is generally considered to be a primary driver of these cycles in a variety of herbivore species. However, weather and climate play a role in entraining cycles over broad landscapes and may alter cyclic dynamics, although the mechanism by which these processes operate is uncertain. Experimental and observational work has suggested that weather influences primary productivity over multi-year time periods, suggesting a pathway through which weather and climate may influence cyclic herbivore dynamics. Using long-term monitoring data, we investigated the relationships among multi-year weather conditions, measures of primary productivity, and the abundance of two cyclic herbivore species: snowshoe hare and northern red-backed vole. We found that precipitation (rain and snow) and growing season temperatures were strongly associated with variation in primary productivity over multi-year time horizons. In turn, fourfold variation in the amplitude of both the hare and vole cycles observed in our study area corresponded to long-term changes in primary productivity. The congruence of our results for these two species suggests a general mechanism by which weather and climate might influence cyclic herbivore population dynamics. Our findings also suggested that the association between climate warming and the disappearance of cycles might be initiated by changes in primary productivity. This work provides an explanation for observed influences of weather and climate on primary productivity and population cycles and will help our collective understanding of how future climate warming may influence these ecological phenomena in the future.PostprintPeer reviewe

Statistical ecology comes of age

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1-4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.Peer reviewe

A strong conditional mutualism limits and enhances seed dispersal and germination of a tropical palm

Seed predation and seed dispersal can have strong effects on early life history stages of plants. These processes have often been studied as individual effects, but the degree to which their relative importance co-varies with seed predator abundance and how this influences seed germination rates is poorly understood. Therefore, we used a combination of observations and field experiments to determine the degree to which germination rates of the palm Astrocaryum mexicanum varied with abundance of a small mammal seed predator/disperser, Heteromysdesmarestianus, in a lowland tropical forest. Patterns of abundance of the two species were strongly related; density of H. desmarestianus was low in sites with low density of A. mexicanum and vice versa. Rates of predation and dispersal of A. mexicanum seeds depended on abundance of H. desmarestianus; sites with high densities of H. desmarestianus had the highest rates of seed predation and lowest rates of seed germination, but a greater total number of seeds were dispersed and there was greater density of seedlings, saplings, and adults of A. mexicanum in these sites. When abundance of H. desmarestianus was experimentally reduced, rates of seed predation decreased, but so did dispersal of A. mexicanum seeds. Critically, rates of germination of dispersed seeds were 5 times greater than undispersed seeds. The results suggest that the relationship between A. mexicanum and H. desmarestianus is a conditional mutualism that results in a strong local effect on the abundance of each species. However, the magnitude and direction of these effects are determined by the relative strength of opposing, but related, mechanisms. A. mexicanum nuts provide H. desmarestianus with a critical food resource, and while seed predation on A. mexicanum nuts by H. desmarestianus is very intense, A. mexicanum ultimately benefits because of the relatively high germination rates of its seeds that are dispersed by H. desmarestianus

The Shark Assemblage at French Frigate Shoals Atoll, Hawai‘i: Species Composition, Abundance and Habitat Use

Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao Mh ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289–1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling

Non-uniform coverage estimators for distance sampling.

Previously in the University eprints HAIRST pilot service at http://eprints.st-andrews.ac.uk/archive/00000445/Allocation of sampling effort in the context of distance sampling is considered. Specifically, allocation of effort in proportion to portions of the survey region that likely contain high concentrations of animals are explored. The probability of a portion of the survey region being included in the sample is proportional to the estimated number of animals in that portion. These estimated numbers of animals may be derived from a density surface model. This results in unequal coverage probability, and a Horvitz- Thompson like estimator can be used to estimate population abundance. The properties of this estimator is explored here via simulation. The benefits, measured in terms of increased precision over traditional equal coverage probability estimators, are meagre, and largely manifested when the underlying population distribution is a smooth gradient.Postprin